UTSW NGS Clinical LaboratoryRoom EB3.302 BioCenter At Southwestern Medical District 2330 Inwood Road Dallas, TX 75390 CLIA ID 45D0861764 Director: Ravi Sarode, MD

1385-Gene Pan-Cancer Muta t ion TestName BOB ZZZTEST MRN 99999999 DOB 01 Jan 2001

Sex Male

Order #

Lab Accession #

Report Accession #

Tumor Specimen #

Germline Specimen #

Ordered by Robert Reed

Institution UTSW NGS Clinical Laboratory

Tumor Tissue Blood

Germline tissue Saliva

ICD-10-CM Acute myeloblastic leukemia, not having achieved

remission

Clinical Stage

Treatment Status

Order Date 31 Aug 2017

Tumor Collection Date 31 Aug 2017

Lab Received Date 31 Aug 2017

Report Date 08 Sep 2017

Report electronically signed by

Andrew Quinn

TREATMENT OPTIONS SUMMARY Gene Sequence Change Aberration FDA approved

within indication FDA approved outside of indication

Clinical Trials

ERBB2 c.929C>T p.Ser310Phe None Ado-trastuzumab emtansine, Afatinib, Neratinib, Lapatinib, Pertuzumab and Trastuzumab

2

FINAL INTERPRETATION

ERBB2 mutation is unambiguously detected with a MAF of ~23%. While there are no FDA approved therapies, there are a number of possible treatments outside of this indication and serval ongoing clinical trials.

Gene ERBB2 Aberration p.Ser310Phe Tumor Allele Frequency 23.34%

Coordinate chr17:37868208

Transcript ID NM_004448

NP_Number NP_004439.2

Variant Qualifier Test

THERAPY MATCH Test

FDA Approved therapy within indication Test No available data FDA Approved therapy outside this indication Ado-trastuzumab emtansine, Afatinib, Neratinib, Lapatinib, Pertuzumab and Trastuzumab Treatment approach Activating ERBB2 alterations may predict sensitivity to Her-targeted drug therapies. A number of therapies, including

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antibodies, small molecule inhibitors, and tyrosine kinase inhibitors, have been FDA-approved in various indications; these and other agents are under investigation (20728210, 19959074, 22149875, 23020162, 25779558, 23816960, 26156651). Resistance and Interactions Several preclinical studies in various tumor types have reported an association between Her2 and chemo- and radio-resistance; similar results have been reported from clinical trials in some tumor types (10096569, 9247307, 12761490, 23524864).

CLINICAL TRIAL MATCH Test 1. A Phase I/II Study of Neratinib in Pediatric Patients With Relapsed or Refractory Solid Tumors or HematologicMalignancies (POE16-01)

Location 205 E 64th St, New York, NY 10065, USA Recruiting

Contact Tanya Trippett, MD 212-639-8267 NCT02932280

2. Individualized Treatment for Relapsed/Refractory Acute Leukemia Based on Chemosensitivity and Genomics/GeneExpression Data

Location 1100 Fairview Ave N, Seattle, WA 98109, USA Recruiting

Contact Pamela S. Becker 206-616-1589 pbecker@u.washington.edu NCT02551718

None Available. Test

INFORMATION ABOUT ERBB2 p.Ser310Phe Test

Activation of ERBB2 by amplification or mutation has been reported to play a role in several types of cancer (23630663). ERBB2 S310F is a missense alteration located in the extracellular domain of the Her2 protein (UniProt). This alteration has been reported to result in activation of Her2 and to be oncogenic, leading to anchorage-independent growth in cells (23630663, 24192927, 26243863, 22908275). ERBB2 S310F has also been reported to confer sensitivity to Her2 inhibitors, including trastuzumab, afatinib, and neratinib; one study of a breast cancer patient harboring the S310F mutation reported Her2 dimerization and a prolonged response to the combination of trastuzumab, pertuzumab, and fulvestrant (26243863, 26358791, 22908275). Test

UNCHARACTERIZED VARIANTS Test HGNC Gene

Amino Acid Change

Location Coordinate Aberration Type Tumor Read Depth

Tumor Allele Frequency

SPEN p.Val1836Met exonic chr1:16258241 Nonsynonymous SNV 1398 48.64%

ATM p.Val2439Ala exonic chr11:108200949 Nonsynonymous SNV 678 46.17%

PRSS8 p.Arg25Trp exonic chr16:31146739 MNV 259 36.68%

PRSS8 p.Arg25Trp exonic chr16:31146747 Nonsynonymous SNV 315 40.32%

ERBB2 p.Asp277Gly exonic chr17:37866663 Nonsynonymous SNV 654 27.52%

PBRM1 p.Thr1380Asn exonic chr3:52597345 Nonsynonymous SNV 631 44.53%

ROS1 p.Gly1027Asp exonic chr6:117686261 Nonsynonymous SNV 1042 48.27%

COMMENTS

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INFORMATION ABOUT THE TEST Test Characteristics and Performance:

DNA and RNA are isolated from fresh or formalin-fixed, paraffin-embedded tissues. Sequencing libraries are generated using Kapa Biosystems and Illumina chemistry. A custom panel of DNA probes is used to produce an enriched library containing all exons from over 1.385 cancer-related genes, which are sequenced on Illumina HiSeq 4000, NextSeq 550 or MiSeq instruments. DNA and RNA sequence analyses are done using custom germline, somatic and mRNA bioinformatics pipelines run on the UTSW Bio-High Performance Computer cluster and optimized for detection of single nucleotide variants, indels and known gene fusions. Reports are generated in the Philips IntelliSpace Genomics system (Philips Healthcare, 2 Canal Park, Cambridge, MA).

Median target exon coverage for the assay is 900X with 94% of exons at >100X. The minor allele frequency limit of detection is 5% for single nucleotide variants and 10% for indels and known gene fusions. The assay is not informative for mutations outside the 1.385 cancer-related genes or for those regions for which the assay achieves limited coverage. Full details of the genes tested, exon coverage and the bioinformatics pipeline are available at http://www.utsouthwestern.edu/sites/genomics-molecular-pathology/.

Disclaimer:

This is a laboratory developed test, and its performance characteristics have been determined by the Next Generation Sequencing Clinical Lab, Department of Pathology, UTSW. It has not been cleared or approved by the U.S. Food and Drug Administration. The U.S. Food and Drug Administration does not require this test to go through premarket review. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments (1988) as qualified to perform high complexity testing.

N-of-One has provided Philips with the research, analysis, and interpretation on a patient specific basis, of peer-reviewed studies and publically available databases. N-of-One does not provide medical services, nor is any N-of-One employee engaged in the practice of medicine for or on behalf of N-of-One. Some tests, drugs and biomarkers identified in this report may not be approved by the FDA for a particular use or validated for that use. The Content is compiled from sources believed to be reliable. Extensive efforts have been made to make the Content as accurate and as up-to-date as possible. The Content may contain typographical errors and omissions. The Content is for research, professional medical and scientific use only. Copyright N-of-One, Inc. 2011-2017: Not for Distribution, Publication or Re-publication.

Builds and Versions

UCSC: v.20130630 dbNSFP: v.3.2a COSMIC: v81 CLINVAR: v.20161201 VARDB: v.20170901 COSMIC_FUSION: v81 THERAPY_AVAILABILITY: v.20170614 Ensembl-vep: v.89.4

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